生物信息学
生物信息學
생물신식학
BIOINFORMATICS
2014年
4期
257-262
,共6页
王立山%祝鹏飞%祁福娟%曹鑫恺%孔艳%臧卫东
王立山%祝鵬飛%祁福娟%曹鑫愷%孔豔%臧衛東
왕립산%축붕비%기복연%조흠개%공염%장위동
野生型p53乳腺癌MCF7细胞%p53%ChIP-seq数据%通路富集分析%蛋白互作网络
野生型p53乳腺癌MCF7細胞%p53%ChIP-seq數據%通路富集分析%蛋白互作網絡
야생형p53유선암MCF7세포%p53%ChIP-seq수거%통로부집분석%단백호작망락
p53-WT MCF-7 breast cancer cells%p53-mediated tumor suppression%ChIP-seq data%Bioinformatics pathway enrichment analysis%Protein-protein interaction network
采用生物信息学方法分析野生型p53乳腺癌MCF7细胞的ChIP-seq(染色质免疫共沉淀-测序)数据,以揭示p53的抑癌分子机制。从NCBI下载的编号为GSE47041的ChIP-seq数据来源于三组试验,分别为：未经处理的乳腺癌MCF7细胞对照( NS_input),Nutlin-3a(一种MDM2拮抗剂)处理的MCF7细胞对照( S_input)和Nutlin-3a刺激MCF7细胞后加入p53抗体的实验组( S_p53)。 ChIP 获得的DNA数据的测序平台为Illumina HiSeq 2000。利用Bowtie参照人基因组hg19进行序列比对；利用MACS进行峰信号检测,并利用自定义软件筛选p53可能的靶基因；利用DAVID在线工具对靶基因进行通路富集分析；最后利用STRING构建蛋白互作网络。研究共得到50个p53的靶基因,其中8个靶基因( CDKN1A、BBC3、BAX、DDB2、MDM2、CCNG1、XPC和PCNA)分别富集到p53信号转导通路和核苷酸切除修复通路两个通路上。在得到的由19个靶基因构成的蛋白质相互作用网络中,连通度最高的前5个基因分别是PCNA、MDM2、REV3L、CDKN1A和BAX。研究中采用的分析ChIP-seq数据的方法能有效揭示野生型p53乳腺癌MCF7细胞中Nutlin-3a激活的p53的抑癌分子机制。
採用生物信息學方法分析野生型p53乳腺癌MCF7細胞的ChIP-seq(染色質免疫共沉澱-測序)數據,以揭示p53的抑癌分子機製。從NCBI下載的編號為GSE47041的ChIP-seq數據來源于三組試驗,分彆為：未經處理的乳腺癌MCF7細胞對照( NS_input),Nutlin-3a(一種MDM2拮抗劑)處理的MCF7細胞對照( S_input)和Nutlin-3a刺激MCF7細胞後加入p53抗體的實驗組( S_p53)。 ChIP 穫得的DNA數據的測序平檯為Illumina HiSeq 2000。利用Bowtie參照人基因組hg19進行序列比對；利用MACS進行峰信號檢測,併利用自定義軟件篩選p53可能的靶基因；利用DAVID在線工具對靶基因進行通路富集分析；最後利用STRING構建蛋白互作網絡。研究共得到50箇p53的靶基因,其中8箇靶基因( CDKN1A、BBC3、BAX、DDB2、MDM2、CCNG1、XPC和PCNA)分彆富集到p53信號轉導通路和覈苷痠切除脩複通路兩箇通路上。在得到的由19箇靶基因構成的蛋白質相互作用網絡中,連通度最高的前5箇基因分彆是PCNA、MDM2、REV3L、CDKN1A和BAX。研究中採用的分析ChIP-seq數據的方法能有效揭示野生型p53乳腺癌MCF7細胞中Nutlin-3a激活的p53的抑癌分子機製。
채용생물신식학방법분석야생형p53유선암MCF7세포적ChIP-seq(염색질면역공침정-측서)수거,이게시p53적억암분자궤제。종NCBI하재적편호위GSE47041적ChIP-seq수거래원우삼조시험,분별위：미경처리적유선암MCF7세포대조( NS_input),Nutlin-3a(일충MDM2길항제)처리적MCF7세포대조( S_input)화Nutlin-3a자격MCF7세포후가입p53항체적실험조( S_p53)。 ChIP 획득적DNA수거적측서평태위Illumina HiSeq 2000。이용Bowtie삼조인기인조hg19진행서렬비대；이용MACS진행봉신호검측,병이용자정의연건사선p53가능적파기인；이용DAVID재선공구대파기인진행통로부집분석；최후이용STRING구건단백호작망락。연구공득도50개p53적파기인,기중8개파기인( CDKN1A、BBC3、BAX、DDB2、MDM2、CCNG1、XPC화PCNA)분별부집도p53신호전도통로화핵감산절제수복통로량개통로상。재득도적유19개파기인구성적단백질상호작용망락중,련통도최고적전5개기인분별시PCNA、MDM2、REV3L、CDKN1A화BAX。연구중채용적분석ChIP-seq수거적방법능유효게시야생형p53유선암MCF7세포중Nutlin-3a격활적p53적억암분자궤제。
To unveilthe molecular mechanism of p53-mediated tumor suppression in p53-WT breast cancervia analyzing ChIP-seq (chromatin immunoprecipitation-sequencing) data by bioinformatics methods. ChIP-Seq dataset GSE47041 was downloaded from Gene Expression Omnibus, which includes three groups of samples:untreatedMCF-7 cells (NS_input), MCF-7 cells treated with a Mdm2 antagonist Nutlin-3a ( S_input ) , Nutlin-3a-treated MCF-7 cells plus p53 antibody treatment (S_p53).The obtained DNA fragments were sequenced using the Illumina HiSeq 2000 platform. Sequence alignment was performed with reference to hg19 using Bowtie; peak calling was performed using MACS; a self-programmed software was used to detect p53 target genes. A total of 50 p53 target genes were predicted. Among them, eight (CDKN1A, BBC3, BAX, DDB2, MDM2, CCNG1,XPC and PCNA) were enriched in p53 signaling transduction pathway and nucleotide excision repairing pathways respectively. A protein-protein interaction network consisting of 19 target genes was obtained;PCNA, MDM2, REV3L, CDKN1A and BAX were the top five genes with the highest degrees of connection. The methods recruited to investigate the molecular mechanism underlying p53-mediated tumor suppression in p53-WT MCF-7 breast cancer cells based on ChIP-seq data are proven feasible and reliable.
